Use the exists_function (isfile or isdir) when checking RMG libs

[alongd]

To properly remove a library (thermo or kinetics, respectively) if they still do not exist

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 0% with 1 line in your changes missing coverage. Please review.

Project coverage is 47.36%. Comparing base (3d7457f) to head (e8c4caf).

Files	Patch %	Lines
t3/main.py	0.00%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #157   +/-   ##
=======================================
  Coverage   47.36%   47.36%           
=======================================
  Files          25       25           
  Lines        3393     3393           
  Branches      914      914           
=======================================
  Hits         1607     1607           
  Misses       1583     1583           
  Partials      203      203           

Flag	Coverage Δ
unittests	47.36% <0.00%> (ø)

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[NellyMitnik]

T3 creates the files for first iteration of RMG, RMG doesn't even run and then T3 fails since species_dictionary.txt can't be found.

  File "/home/nellymitnik/Code/T3/T3.py", line 73, in <module>
    main()
  File "/home/nellymitnik/Code/T3/T3.py", line 69, in main
    t3_object.execute()
  File "/home/nellymitnik/Code/T3/t3/main.py", line 305, in execute
    global_observables=None,
  File "/home/nellymitnik/Code/T3/t3/simulate/factory.py", line 83, in simulate_factory
    global_observables=global_observables,
  File "/home/nellymitnik/Code/T3/t3/simulate/rmg_constantTP.py", line 96, in __init__
    self.set_up()
  File "/home/nellymitnik/Code/T3/t3/simulate/rmg_constantTP.py", line 139, in set_up
    check_duplicates=False,
  File "/home/nellymitnik/Code/RMG-Py/rmgpy/tools/loader.py", line 86, in load_rmg_py_job
    check_duplicates=check_duplicates)
  File "rmgpy/chemkin.pyx", line 982, in rmgpy.chemkin.load_chemkin_file
  File "rmgpy/chemkin.pyx", line 872, in rmgpy.chemkin.load_species_dictionary
FileNotFoundError: [Errno 2] No such file or directory: '/home/nellymitnik/runs/T3/2BF/xmr_2057_1/iteration_1/RMG/chemkin/species_dictionary.txt'```

[alongd]

@NellyMitnik, It runs fine for me. Let's discuss it offline and see the run files